title: Mapping the small RNA content of simian immunodeficiency virions (SIV).
abstract: Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
authors.affiliation:   Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Brameier
authors.forename: Wiebke
authors.initials: W
authors.lastname: Ibing
authors.forename: Katharina
authors.initials: K
authors.lastname: Höfer
authors.forename: Judith
authors.initials: J
authors.lastname: Montag
authors.forename: Christiane
authors.initials: C
authors.lastname: Stahl-Hennig
authors.forename: Dirk
authors.initials: D
authors.lastname: Motzkus
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D055354:Exosomes / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D020733:RNA, Small Cytoplasmic / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism; D012357:RNA, Transfer, Lys / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D018271:Signal Recognition Particle / Q000235:genetics / Q000378:metabolism; D015302:Simian Immunodeficiency Virus / Q000235:genetics*; D014771:Virion / Q000235:genetics*
chemical_list: C115990:7SL RNA; D035683:MicroRNAs; D012335:RNA, Ribosomal; D020733:RNA, Small Cytoplasmic; D020537:RNA, Small Nucleolar; D012357:RNA, Transfer, Lys; D022661:RNA, Untranslated; D012367:RNA, Viral; D018271:Signal Recognition Particle